Polygenic Score (PGS) ID: PGS001526

Predicted Trait
Reported Trait QT interval
Mapped Trait(s) QT interval (EFO_0004682)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI22331
Released in PGS Catalog: Nov. 25, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_INI22331
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 609
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
14,051 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 14,051 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM005305 PSS004971|
African Ancestry|
120 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: QT interval — — R²: 0.07804 [0.06552, 0.09056]
Incremental R2 (full-covars): -0.0033
PGS R2 (no covariates): 0.00046 [-0.00058, 0.0015]		 age, sex, UKB array type, Genotype PCs —
PPM005306 PSS004972|
East Asian Ancestry|
68 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: QT interval — — R²: 0.32528 [0.28882, 0.36175]
Incremental R2 (full-covars): 0.0416
PGS R2 (no covariates): 0.07506 [0.05104, 0.09907]		 age, sex, UKB array type, Genotype PCs —
PPM005307 PSS004973|
European Ancestry|
872 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: QT interval — — R²: 0.05819 [0.05255, 0.06383]
Incremental R2 (full-covars): 0.02543
PGS R2 (no covariates): 0.02774 [0.02372, 0.03176]		 age, sex, UKB array type, Genotype PCs —
PPM005308 PSS004974|
South Asian Ancestry|
201 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: QT interval — — R²: 0.06747 [0.05675, 0.0782]
Incremental R2 (full-covars): -0.0012
PGS R2 (no covariates): 0.0053 [0.0021, 0.00851]		 age, sex, UKB array type, Genotype PCs —
PPM005309 PSS004975|
European Ancestry|
3,523 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: QT interval — — R²: 0.01777 [0.01579, 0.01974]
Incremental R2 (full-covars): 0.01493
PGS R2 (no covariates): 0.01503 [0.01321, 0.01685]		 age, sex, UKB array type, Genotype PCs —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS004971 — — 120 individuals — African unspecified — UKB —
PSS004972 — — 68 individuals — East Asian — UKB —
PSS004973 — — 872 individuals — European non-white British ancestry UKB —
PSS004974 — — 201 individuals — South Asian — UKB —
PSS004975 — — 3,523 individuals — European white British ancestry UKB Testing cohort (heldout set)